From 142fbe1b1776a94b610705d77e297bee03a60579 Mon Sep 17 00:00:00 2001 From: polarbean <harry.carey95@gmail.com> Date: Mon, 24 Mar 2025 17:30:53 +0100 Subject: [PATCH] include link to QCalign --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index c63d952..0c1909e 100644 --- a/README.md +++ b/README.md @@ -63,7 +63,7 @@ PyNutil generates a series of reports in the folder which you specify. ## Per-Hemisphere Quantification If you use an atlas which has a hemisphere map (All brainglobe atlases have this, it is a volume in the shape of the atlas with 1 in the lft hemisphere and 2 in the right) PyNutil will generate per-hemisphere quantifications in addition to total numbers. In addition, PyNutil will also genearte additional per-hemisphere point cloud files for viewing in meshview. ## Damage Quantification -The QCAlign tool allows you to mark damaged areas on your section. This means that these damaged areas are excluded from your point clouds. In addition, PyNutil will seperately quantify damaged and undamaged areas. Note the undamaged, and damaged column names. +[The QCAlign tool](https://www.nitrc.org/projects/qcalign) allows you to mark damaged areas on your section. This means that these damaged areas are excluded from your point clouds. In addition, PyNutil will seperately quantify damaged and undamaged areas. Note the undamaged, and damaged column names. # Meshview json files PyNutil will produce meshview json files. This can be opened in [MeshView for the Allen Mouse](https://meshview.apps.ebrains.eu/?atlas=ABA_Mouse_CCFv3_2017_25um) or for [the Waxholm Rat](https://meshview.apps.ebrains.eu/) -- GitLab